The WinHelp and HTML formats in Author-it do not support multi-level heading numbering; numbering will only work in the printed Word output. Author-it's editing environment does not currently display multi-level heading numbering.
To publish a book with chapters that contain numbered sections and numbered subsections (Chapter 1 - 1. Section - 1.1 Subsection 1.2, and so forth), define multi-level numbering in the Heading styles in the Word Publishing template used to create the printed output. Read Word's user documentation for details.